Agricultural land use induces broader homogenization of soil microbial functional composition than taxonomic composition

Land-use changes from natural ecosystems to farmlands significantly alter soil functioning worldwide, especially challenging sub-Saharan Africa with rapid population growth and intensive agriculture. Soil microbial diversity is vital in supporting ecosystem multifunctionality and preventing pathogen growth. Recent studies have revealed that farming activities homogenize microbial communities across distant sites, which may lead to functional homogenization on that scale. However, given the redundancy of microbial functions, functional homogenization driven by farming may occur on a broader scale than taxonomic homogenization. We compared the taxonomic and functional compositions of soil prokaryotic and fungal communities between natural lands and farmlands at scales ranging from within-site (~200 m) to across-site (~1500 km) in Kenya and Malawi, using amplicon sequencing of 16S rRNA and ITS genes and the prediction of microbial functions. Soil microbial functional compositions were homogenized more broadly than taxonomic compositions in farmlands compared to natural lands, suggesting that similar functional responses to farming occur across scales where different taxa thrive. Furthermore, environmental factors predominantly influenced within-site homogeneity, whereas farming itself was a significant contributor to across-site homogeneity, indicating an overriding influence of farming compared to environmental variations. Additionally, pathogenic fungi were relatively more abundant in farmlands, likely due to reduced species competition and farming-induced environmental changes such as low soil pH. Our findings highlight the need to investigate microbial functional diversity alongside taxonomic diversity when assessing the impacts of land-use changes on soil health to develop sustainable land management strategies.